I am trying to debug a problem with a package I am deploying that uses the conda-forge

I checked the pynco dependencies, they don't include gsl. </blockquot

and my conda list: <div class="snippet-clipboard-content notranslate position-rela

and my .condarc: <div class="snippet-clipboard-content notranslate position-relati

Problem running ncks from conda-forge pynco installation about pynco-feedstock HOT 14 CLOSED

conda-forge commented on July 4, 2024

Problem running ncks from conda-forge pynco installation

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Comments (14)

ocefpaf commented on July 4, 2024

I checked the pynco dependencies, they don't include gsl.

pynco does not but nco does and pynco depends on that.

Can you send me the results of your conda info, conda list for that env and cat ~/.condarc?

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mjbrodzik commented on July 4, 2024

Hi, thanks for fast response, yes, here is my conda info

(testpynco) vpn-nsidc227-dhcp:~ brodzik$ conda info
Current conda install:

           platform : osx-64
      conda version : 4.3.22
   conda is private : False
  conda-env version : 4.3.22
conda-build version : not installed
     python version : 2.7.12.final.0
   requests version : 2.18.1
   root environment : /opt/miniconda  (read only)
default environment : /Users/brodzik/.conda/envs/testpynco
   envs directories : /Users/brodzik/.conda/envs
                      /opt/miniconda/envs
      package cache : /opt/miniconda/pkgs
                      /Users/brodzik/.conda/pkgs
       channel URLs : https://conda.anaconda.org/nsidc/channel/main/osx-64
                      https://conda.anaconda.org/nsidc/channel/main/noarch
                      https://conda.anaconda.org/nsidc/channel/dev/osx-64
                      https://conda.anaconda.org/nsidc/channel/dev/noarch
                      https://conda.anaconda.org/conda-forge/channel/main/osx-64
                      https://conda.anaconda.org/conda-forge/channel/main/noarch
                      https://repo.continuum.io/pkgs/free/osx-64
                      https://repo.continuum.io/pkgs/free/noarch
                      https://repo.continuum.io/pkgs/r/osx-64
                      https://repo.continuum.io/pkgs/r/noarch
                      https://repo.continuum.io/pkgs/pro/osx-64
                      https://repo.continuum.io/pkgs/pro/noarch
        config file : /Users/brodzik/.condarc
         netrc file : None
       offline mode : False
         user-agent : conda/4.3.22 requests/2.18.1 CPython/2.7.12 Darwin/16.7.0 OSX/10.12.6    
            UID:GID : 13159:200

(testpynco) vpn-nsidc227-dhcp:~ brodzik$

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mjbrodzik commented on July 4, 2024

and my conda list:

(testpynco) vpn-nsidc227-dhcp:~ brodzik$ conda list
# packages in environment at /Users/brodzik/.conda/envs/testpynco:
#
ca-certificates           2017.7.27.1                   0    conda-forge/channel/main
certifi                   2017.7.27.1              py36_0    conda-forge/channel/main
curl                      7.54.1                        0    conda-forge/channel/main
esmf                      7.0.0                         6    conda-forge/channel/main
expat                     2.2.1                         0    conda-forge/channel/main
gsl                       2.1                           2    conda-forge/channel/main
h5py                      2.7.1                    py36_1    conda-forge/channel/main
hdf4                      4.2.12                        0    conda-forge/channel/main
hdf5                      1.8.18                        0    conda-forge/channel/main
jpeg                      9b                            1    conda-forge/channel/main
krb5                      1.14.2                        0    conda-forge/channel/main
libgcc                    4.8.5                         1    defaults
libgfortran               3.0.0                         0    conda-forge/channel/main
libnetcdf                 4.4.1.1                       5    conda-forge/channel/main
libssh2                   1.8.0                         1    conda-forge/channel/main
mkl                       2017.0.3                      0    defaults
mpich                     3.2                           5    conda-forge/channel/main
nco                       4.6.9                         0    conda-forge/channel/main
ncurses                   5.9                          10    conda-forge/channel/main
netcdf-fortran            4.4.4                         3    conda-forge/channel/main
netcdf4                   1.3.0                    py36_0    conda-forge/channel/main
numpy                     1.13.1                   py36_0    defaults
openblas                  0.2.19                        2    conda-forge/channel/main
openssl                   1.0.2l                        0    conda-forge/channel/main
pip                       9.0.1                    py36_0    conda-forge/channel/main
pynco                     0.0.3                    py36_0    conda-forge/channel/main
python                    3.6.2                         0    conda-forge/channel/main
python-dateutil           2.6.1                    py36_0    conda-forge/channel/main
readline                  6.2                           0    conda-forge/channel/main
scipy                     0.19.1              np113py36_0    defaults
setuptools                36.3.0                   py36_0    conda-forge/channel/main
six                       1.11.0                   py36_1    conda-forge/channel/main
sqlite                    3.13.0                        1    conda-forge/channel/main
tk                        8.5.19                        2    conda-forge/channel/main
udunits2                  2.2.23                        1    conda-forge/channel/main
wheel                     0.30.0                     py_1    conda-forge/channel/main
xz                        5.2.3                         0    conda-forge/channel/main
zlib                      1.2.11                        0    conda-forge/channel/main
(testpynco) vpn-nsidc227-dhcp:~ brodzik$

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mjbrodzik commented on July 4, 2024

and my .condarc:

(testpynco) vpn-nsidc227-dhcp:~ brodzik$ more ~/.condarc
channels:
  - https://conda.anaconda.org/nsidc/channel/main
  - https://conda.anaconda.org/nsidc/channel/dev
  - https://conda.anaconda.org/conda-forge/channel/main
  - defaults
always_yes: 'True'
show_channel_urls: 'True'
(testpynco) vpn-nsidc227-dhcp:~ brodzik$

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mjbrodzik commented on July 4, 2024

(is there some way to do better block quotes in github markdown?)

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ocefpaf commented on July 4, 2024

You are using 3 channels and two are on top of conda-forge, that may be the source of the issue.
However, I do not see any package from those channels installed in the env :-/

Note that gsl was installed, 6th line on your conda list result, but that is not the right version.
I'll try to inspect the package and see why that happened, meanwhile can you try force conda install gsl=2.2.1 there and see if it fixes the issue?

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ocefpaf commented on July 4, 2024

(is there some way to do better block quotes in github markdown?)

I usually use gist links to for large outputs, or even attached files.

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mjbrodzik commented on July 4, 2024

Yes, the extra channels are for the packages we deploy from NSIDC--Nothing's installed from there for this example because I was trying to isolate the issue.

In the testgdal env, if I do:

conda install gsl=2.2

it installed gsl and also upgraded scipy and numpy to [blas-openblas]:

gsl:   2.1-2              conda-forge/channel/main --> 2.2.1-blas_openblas_2         conda-for\
ge/channel/main [blas_openblas]                                                                    
    numpy: 1.13.1-py36_0      defaults                 --> 1.13.1-py36_blas_openblas_200 conda-for\
ge/channel/main [blas_openblas]                                                                    
    scipy: 0.19.1-np113py36_0 defaults                 --> 0.19.1-py36_blas_openblas_202 conda-for\
ge/channel/main [blas_openblas]

after that I was able to run ncks without the error.

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ocefpaf commented on July 4, 2024

after that I was able to run ncks without the error.

Cool! I'll close this and conda-forge/nco-feedstock#44 should fix it for good.

Thanks for the report!

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mjbrodzik commented on July 4, 2024

Felipe, I have one more question, I'm a little new to conda packaging. How will I be able to tell when your pull request makes it into nco? MJ

On Thu, 28 Sep 2017, Filipe wrote: Date: Thu, 28 Sep 2017 12:34:43 -0700 From: Filipe ***@***.***> Reply-To: conda-forge/pynco-feedstock <reply+004c8ae82dc7075c189c16614aa3df6cf10d61f6c0e30a7a92cf0000000115e510d ***@***.***> To: conda-forge/pynco-feedstock ***@***.***> Cc: Mary Jo Brodzik ***@***.***>, Author ***@***.***> Subject: Re: [conda-forge/pynco-feedstock] Problem running ncks from conda-forge pynco installation (#7) after that I was able to run ncks without the error. Cool! I'll close this and conda-forge/nco-feedstock#44 should fix it for good. Thanks for the report! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.[AEyK6O7ePZYIHODOhRgl-qBU4LIlqytkks5sm_TTgaJpZM4Pnq-1.gif]

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Mary Jo Brodzik, Senior Associate Scientist, 303-492-8263 NSIDC/CIRES, Univ. of Colo. at Boulder, 449 UCB, Boulder, CO 80309-0449 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ "We cannot solve our problems with the same thinking we used when we created them." --Albert Einstein

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mjbrodzik commented on July 4, 2024

And in my package, will it mean I have to pin gsl? or nco? or pynco? in my package? Right now I just have pynco pinned to <=0.0.3,<0.1.0, but I don't know whether this the correct way to do this.

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ocefpaf commented on July 4, 2024

You can 'watch' the repo to know when the PR is merged and then click on the CIs build job for the platform you are interested.

It should be up latet today or early tomorrow though.

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mjbrodzik commented on July 4, 2024

Thanks and I see you just merged it. I really appreciate your help and willingness to explain. Mary Jo

On Thu, 28 Sep 2017, Filipe wrote: Date: Thu, 28 Sep 2017 20:26:51 +0000 (UTC) From: Filipe ***@***.***> Reply-To: conda-forge/pynco-feedstock <reply+004c8ae84d01b815f9f1b2ae3b602a787588d722d23860ed92cf0000000115e51d0 ***@***.***> To: conda-forge/pynco-feedstock ***@***.***> Cc: Mary Jo Brodzik ***@***.***>, Author ***@***.***> Subject: Re: [conda-forge/pynco-feedstock] Problem running ncks from conda-forge pynco installation (#7) You can 'watch' the repo to know when the PR is merged and then click on the CIs build job for the platform you are interested. It should be up latet today or early tomorrow though. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.[AEyK6KJm0mVvSH7jmYvyCHivEzS4_C3Hks5snAELgaJpZM4Pnq-1.gif]

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ocefpaf commented on July 4, 2024

Thanks and I see you just merged it. I really appreciate your help and
willingness to explain.

No problem. As soon as https://travis-ci.org/conda-forge/nco-feedstock/builds/281040065 finishes the OS X package will be available. (The Linux package is already in the channel.)

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Problem running ncks from conda-forge pynco installation about pynco-feedstock HOT 14 CLOSED

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